This repository stores the codes that run SLiM simulations and plot the graphs for the paper that predicts the genomic resolution of Bulk Segregant Analysis (BSA).
predict_bsa_resolution.py is the python script that can be used to calculate the expected genomic resolution of a BSA experiment based on the analytical solutions derived in our paper. No additional python package is needed to run the script. The python script takes five arguments in order: the estimated effective population size Ne, the length of the experiment t, the average recombination rate r, the sample size for genome sequencing s and the analytical model used for the calculation integration or recursion. An example is shown below:
python predict_bsa_resolution.py 100 10 1e-8 20 integration uses the integration model to calculate the expected genomic resolution of a BSA experiment with Ne=100, running from F0 to F10, an estimated recombination probablity of 1e-8 and sampling a total of 20 diploid individuals for genome sequencing. The output of running the script would be:
Expected Genomic Resolution of BSA Experiment with Ne=100, Gen=10, R=1.000e-08, s=20 using integration model is: 7.149e+05 bp.